Contacts of the helix formed by residues 37 - 47 (chain A) in PDB entry 4ENM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A MET* 3.6 24.5 - - + +
6A PHE* 3.8 22.9 - + + -
29A ALA* 4.1 2.0 - - - -
34A MET* 2.9 39.8 + - + +
35A PRO 3.2 0.4 - - - -
36A SER* 1.3 94.0 - - - +
38A ALA* 1.3 64.5 + - - +
39A ARG 3.2 2.5 - - - -
40A GLN* 2.9 36.1 + - + +
41A VAL* 3.1 14.8 + - - +
22C C 3.9 15.9 - - - -
23C A 2.2 35.5 + - - -
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Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 4.0 5.0 - - - +
26A GLY* 3.8 21.8 - - - +
29A ALA* 3.9 6.2 - - + +
35A PRO 4.4 3.3 + - - +
36A SER 3.3 5.9 + - - +
37A TYR* 1.3 72.9 - - - +
39A ARG* 1.3 69.1 + - + +
41A VAL* 2.8 24.1 + - - +
42A GLY 3.1 6.6 + - - -
8B C 3.8 28.7 - - - +
9B T 4.1 9.9 - - - -
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Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A SER 5.3 3.4 - - - +
37A TYR 3.2 0.8 - - - -
38A ALA* 1.3 76.1 - - + +
40A GLN* 1.3 71.3 + - - +
42A GLY* 2.8 18.7 + - - -
43A GLN* 3.0 13.6 + - - +
6B G 3.2 62.8 + - + +
8B C 3.4 63.2 - - + +
20C G 4.3 0.4 + - - -
21C C 2.7 57.6 + - + +
22C C 4.3 12.1 - - - +
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Residues in contact with GLN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A MET* 5.4 0.2 - - - -
6A PHE* 3.5 20.6 - - + -
7A TYR* 4.7 2.0 - - + -
36A SER 4.6 0.2 + - - -
37A TYR* 2.9 40.0 + - + +
39A ARG* 1.3 92.2 - - - +
41A VAL* 1.3 59.7 + - - +
43A GLN* 3.0 28.3 + - - +
44A ALA* 2.8 28.8 + - - +
22C C 3.0 36.1 + - - +
23C A 2.8 29.0 + - - +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 4.1 10.8 - - + -
10A VAL* 3.8 24.7 - - + -
25A TYR* 3.6 32.3 - - + +
28A ILE* 4.0 18.4 - - + -
29A ALA* 3.9 14.4 - - + +
37A TYR 3.1 15.5 + - - +
38A ALA* 2.8 10.3 + - - +
40A GLN* 1.3 72.5 - - - +
42A GLY* 1.3 70.2 + - - +
44A ALA* 3.5 5.1 + - - +
45A MET* 3.2 30.7 + - + +
59A VAL* 5.3 1.1 - - + -
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Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A TYR* 4.5 6.7 - - - -
38A ALA 3.1 5.8 + - - -
39A ARG 2.8 10.9 + - - -
41A VAL* 1.3 80.1 - - - +
43A GLN* 1.3 64.9 + - - +
45A MET* 2.9 14.1 + - - +
46A LYS* 3.0 13.4 + - - +
7B BZG 3.8 29.6 - - - +
8B C 4.9 2.0 - - - -
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Residues in contact with GLN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TYR* 2.7 33.5 + - - +
39A ARG 3.0 9.0 + - - +
40A GLN* 3.1 36.3 + - - +
42A GLY* 1.3 73.0 - - - +
44A ALA* 1.3 66.6 + - - +
46A LYS* 3.0 22.8 + - + +
47A HIS* 3.1 25.1 + - + -
6B G 3.9 9.3 + - - +
23C A 3.4 40.9 + - - +
24C T 3.7 10.8 - - - +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 5.3 0.2 - - + -
7A TYR* 4.4 22.1 - - + -
10A VAL* 4.1 16.2 - - + -
11A TYR* 2.8 35.8 + - + +
40A GLN 2.8 14.5 + - - +
41A VAL* 3.6 9.2 - - - +
43A GLN* 1.3 71.2 - - - +
45A MET* 1.3 76.9 + - + +
47A HIS* 3.0 11.8 + - - +
48A LEU 3.5 1.6 + - - -
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Residues in contact with MET 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.5 32.5 - - + -
11A TYR* 4.1 9.6 - - + -
14A VAL* 3.8 14.1 - - + -
25A TYR* 4.6 6.5 - - + -
41A VAL* 3.2 19.5 - - + +
42A GLY 2.9 8.8 + - - +
44A ALA* 1.3 77.7 - - + +
46A LYS* 1.3 55.5 + - - +
47A HIS 2.7 11.6 + - - -
48A LEU* 2.9 28.5 + - - +
54A VAL* 5.4 0.2 - - - -
56A TRP* 4.1 24.2 - - - -
59A VAL* 4.4 13.5 - - + -
7B BZG 3.4 46.0 - - + +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLY 3.0 6.8 + - - +
43A GLN* 3.0 16.2 + - + +
45A MET* 1.3 77.2 - - - +
47A HIS* 1.3 72.4 + - + +
48A LEU 3.5 2.6 - - - +
71A ILE* 3.9 20.1 - - - +
6B G 3.3 37.2 - - - +
7B BZG 3.1 60.5 + - + +
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Residues in contact with HIS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TYR* 3.8 30.8 + + + -
11A TYR* 4.4 6.9 + - - +
43A GLN* 3.1 22.9 + - + -
44A ALA* 3.0 10.5 + - - +
45A MET 2.7 1.8 + - - -
46A LYS* 1.3 95.2 - - + +
48A LEU* 1.3 67.1 + - - +
49A HIS* 4.8 11.4 + - - -
24C T 5.1 11.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il